Starting phenix.real_space_refine
on Mon Jul 28 21:03:50 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7f23_31426/07_2025/7f23_31426.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f23_31426/07_2025/7f23_31426.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f23_31426/07_2025/7f23_31426.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f23_31426/07_2025/7f23_31426.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f23_31426/07_2025/7f23_31426.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f23_31426/07_2025/7f23_31426.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.090
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3063 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      53      5.16       5
     C    5196      2.51       5
     N    1440      2.21       5
     O    1519      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8211
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "F"
      Number of atoms: 2197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2197
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 9, 'TRANS': 266}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1937
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 2629
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 2624
    Chain: "E"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 434
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "F"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'LDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASP B  27 " occ=0.45
      ... (14 atoms not shown)
      pdb=" OD2BASP B  27 " occ=0.55
  Time building chain proxies: 6.33, per 1000 atoms: 0.77
  Number of scatterers: 8211
  At special positions: 0
  Unit cell: (84.786, 95.656, 126.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      53     16.00
     P       3     15.00
     O    1519      8.00
     N    1440      7.00
     C    5196      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.56
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      43.8% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'F' and resid 20 through 51
    Processing helix  chain 'F' and resid 58 through 88
      Proline residue:  F  79  - end of helix
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 4.325A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR F 108 " --> pdb=" O   ILE F 104 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ILE F 111 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
    Processing helix  chain 'F' and resid 136 through 161
      Proline residue:  F 158  - end of helix
    Processing helix  chain 'F' and resid 191 through 203
    Processing helix  chain 'F' and resid 203 through 237
      removed outlier: 3.601A  pdb=" N   ALA F 208 " --> pdb=" O   TYR F 204 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 265 through 298
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.777A  pdb=" N   GLY F 320 " --> pdb=" O   PHE F 316 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   TRP F 321 " --> pdb=" O   VAL F 317 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 346
    Processing helix  chain 'A' and resid 13 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.773A  pdb=" N   PHE A 312 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.264A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.051A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.984A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.507A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.772A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'D' and resid 55 through 59
      removed outlier: 3.571A  pdb=" N   ASN D  59 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 9.365A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.487A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.690A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.904A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.866A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.645A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.783A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.361A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.127A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 4.817A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 2.81 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2681
        1.34 -     1.46: 2060
        1.46 -     1.58: 3567
        1.58 -     1.71: 5
        1.71 -     1.83: 72
  Bond restraints: 8385
  Sorted by residual:
  bond pdb=" N   CYS F  96 "
       pdb=" CA  CYS F  96 "
    ideal  model  delta    sigma   weight residual
    1.458  1.427  0.030 1.33e-02 5.65e+03 5.13e+00
  bond pdb=" CA  SER F 110 "
       pdb=" C   SER F 110 "
    ideal  model  delta    sigma   weight residual
    1.525  1.498  0.027 1.25e-02 6.40e+03 4.68e+00
  bond pdb=" CB  TRP B  99 "
       pdb=" CG  TRP B  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.434  0.064 3.10e-02 1.04e+03 4.22e+00
  bond pdb=" CG  LEU F  66 "
       pdb=" CD1 LEU F  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.15e+00
  bond pdb=" C3  LDP F 501 "
       pdb=" C4  LDP F 501 "
    ideal  model  delta    sigma   weight residual
    1.400  1.361  0.039 2.00e-02 2.50e+03 3.87e+00
  ... (remaining 8380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 11016
        2.51 -     5.01: 312
        5.01 -     7.52: 33
        7.52 -    10.02: 9
       10.02 -    12.53: 1
  Bond angle restraints: 11371
  Sorted by residual:
  angle pdb=" CA  CYS E  99 "
        pdb=" CB  CYS E  99 "
        pdb=" SG  CYS E  99 "
      ideal   model   delta    sigma   weight residual
     114.40  126.93  -12.53 2.30e+00 1.89e-01 2.97e+01
  angle pdb=" C   LYS A 233 "
        pdb=" N   TRP A 234 "
        pdb=" CA  TRP A 234 "
      ideal   model   delta    sigma   weight residual
     121.58  113.52    8.06 1.95e+00 2.63e-01 1.71e+01
  angle pdb=" C   THR F 108 "
        pdb=" N   ALA F 109 "
        pdb=" CA  ALA F 109 "
      ideal   model   delta    sigma   weight residual
     120.72  114.50    6.22 1.67e+00 3.59e-01 1.39e+01
  angle pdb=" C   SER B 334 "
        pdb=" CA  SER B 334 "
        pdb=" CB  SER B 334 "
      ideal   model   delta    sigma   weight residual
     111.63  106.58    5.05 1.36e+00 5.41e-01 1.38e+01
  angle pdb=" C   GLY B 131 "
        pdb=" N   ASN B 132 "
        pdb=" CA  ASN B 132 "
      ideal   model   delta    sigma   weight residual
     122.81  128.33   -5.52 1.57e+00 4.06e-01 1.24e+01
  ... (remaining 11366 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.60: 4895
       34.60 -    69.20: 87
       69.20 -   103.80: 4
      103.80 -   138.40: 1
      138.40 -   173.00: 2
  Dihedral angle restraints: 4989
    sinusoidal: 1958
      harmonic: 3031
  Sorted by residual:
  dihedral pdb=" CB  CYS E  99 "
           pdb=" SG  CYS E  99 "
           pdb=" SG  CYS E 107 "
           pdb=" CB  CYS E 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -18.21  -67.79     1      1.00e+01 1.00e-02 5.97e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -117.73 -173.00     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -36.16  140.75     1      2.00e+01 2.50e-03 4.26e+01
  ... (remaining 4986 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 956
       0.062 -    0.125: 272
       0.125 -    0.187: 48
       0.187 -    0.250: 1
       0.250 -    0.312: 1
  Chirality restraints: 1278
  Sorted by residual:
  chirality pdb=" CA  CYS E  99 "
            pdb=" N   CYS E  99 "
            pdb=" C   CYS E  99 "
            pdb=" CB  CYS E  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  PRO F 206 "
            pdb=" N   PRO F 206 "
            pdb=" C   PRO F 206 "
            pdb=" CB  PRO F 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.53e-01
  chirality pdb=" CA  PHE A 222 "
            pdb=" N   PHE A 222 "
            pdb=" C   PHE A 222 "
            pdb=" CB  PHE A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.58e-01
  ... (remaining 1275 not shown)

  Planarity restraints: 1444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F 109 "   -0.043 2.00e-02 2.50e+03   8.57e-02 7.34e+01
        pdb=" C   ALA F 109 "    0.148 2.00e-02 2.50e+03
        pdb=" O   ALA F 109 "   -0.054 2.00e-02 2.50e+03
        pdb=" N   SER F 110 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER F  94 "   -0.030 2.00e-02 2.50e+03   6.06e-02 3.68e+01
        pdb=" C   SER F  94 "    0.105 2.00e-02 2.50e+03
        pdb=" O   SER F  94 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   PHE F  95 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 347 "   -0.021 2.00e-02 2.50e+03   4.26e-02 1.81e+01
        pdb=" C   ARG A 347 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ARG A 347 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ILE A 348 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1441 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 216
        2.65 -     3.21: 8278
        3.21 -     3.77: 13082
        3.77 -     4.34: 17654
        4.34 -     4.90: 29033
  Nonbonded interactions: 68263
  Sorted by model distance:
  nonbonded pdb=" OG  SER F  65 "
            pdb=" ND2 ASN F 113 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD2 ASP B 333 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER A  54 "
            pdb=" O1G GTP A 401 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" OG1 THR A  55 "
            pdb=" O1A GTP A 401 "
     model   vdw
     2.164 3.040
  ... (remaining 68258 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     24.210
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.068   8388  Z= 0.468
  Angle     :  1.013  12.527  11377  Z= 0.575
  Chirality :  0.057   0.312   1278
  Planarity :  0.007   0.086   1444
  Dihedral  : 15.075 172.997   3016
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.99 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.23), residues: 1025
  helix: -1.68 (0.21), residues: 416
  sheet: -1.41 (0.30), residues: 245
  loop : -1.74 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F  99 
 HIS   0.014   0.002   HIS A 357 
 PHE   0.032   0.003   PHE F 333 
 TYR   0.018   0.002   TYR E  95 
 ARG   0.004   0.001   ARG F 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12964 (  435)
  hydrogen bonds       : angle       6.83344 ( 1251)
  SS BOND              : bond        0.01128 (    3)
  SS BOND              : angle       5.23469 (    6)
  covalent geometry    : bond        0.01034 ( 8385)
  covalent geometry    : angle       1.00598 (11371)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   86 ILE cc_start: 0.8784 (mm) cc_final: 0.8539 (mt)
REVERT: F  194 TYR cc_start: 0.8868 (t80) cc_final: 0.8660 (t80)
REVERT: F  225 ILE cc_start: 0.8842 (mt) cc_final: 0.8642 (mp)
REVERT: A   20 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8067 (mtt-85)
REVERT: A   33 ASP cc_start: 0.8447 (t0) cc_final: 0.8115 (t0)
REVERT: A   35 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: B  214 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6755 (ttp-170)
REVERT: B  269 ILE cc_start: 0.9095 (mt) cc_final: 0.8793 (mm)
REVERT: E   29 PHE cc_start: 0.9027 (t80) cc_final: 0.8697 (t80)
REVERT: E   80 TYR cc_start: 0.7366 (m-80) cc_final: 0.7081 (m-80)
REVERT: E   82 GLN cc_start: 0.7631 (tp40) cc_final: 0.7293 (tp40)
REVERT: E   83 MET cc_start: 0.7743 (ptp) cc_final: 0.7524 (ptp)
REVERT: D   47 GLU cc_start: 0.7750 (pm20) cc_final: 0.6941 (pm20)
  outliers start: 2
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2355
  time to fit residues: 65.1189
Evaluate side-chains
  160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
F  41 ASN
F 113 ASN
F 164 HIS
A  14 ASN
A 267 GLN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B 110 ASN
B 119 ASN
B 220 GLN
B 266 HIS
E  13 GLN
E  77 ASN
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.161361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.120644 restraints weight = 32195.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.123004 restraints weight = 13210.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.124292 restraints weight = 9414.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8388  Z= 0.143
  Angle     :  0.648  12.510  11377  Z= 0.337
  Chirality :  0.045   0.191   1278
  Planarity :  0.004   0.040   1444
  Dihedral  :  9.576 177.611   1155
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.74 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1025
  helix:  0.42 (0.24), residues: 414
  sheet: -0.88 (0.33), residues: 218
  loop : -0.78 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.008   0.001   HIS F  53 
 PHE   0.019   0.001   PHE E 108 
 TYR   0.013   0.001   TYR F 122 
 ARG   0.004   0.000   ARG E  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04808 (  435)
  hydrogen bonds       : angle       5.06402 ( 1251)
  SS BOND              : bond        0.00683 (    3)
  SS BOND              : angle       4.09106 (    6)
  covalent geometry    : bond        0.00303 ( 8385)
  covalent geometry    : angle       0.64150 (11371)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  210 MET cc_start: 0.6321 (mtp) cc_final: 0.5763 (ttm)
REVERT: F  211 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7497 (mt)
REVERT: F  271 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8905 (mm)
REVERT: F  333 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7876 (m-10)
REVERT: A   33 ASP cc_start: 0.8488 (t0) cc_final: 0.8134 (t0)
REVERT: A  249 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7631 (p0)
REVERT: A  356 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8216 (mtm180)
REVERT: B   46 ARG cc_start: 0.7541 (mtp85) cc_final: 0.6996 (mtm110)
REVERT: B  211 TRP cc_start: 0.7605 (m100) cc_final: 0.7347 (m100)
REVERT: B  214 ARG cc_start: 0.7305 (mtm180) cc_final: 0.7007 (ptp-170)
REVERT: E    4 LEU cc_start: 0.8090 (mt) cc_final: 0.7874 (mt)
REVERT: E   29 PHE cc_start: 0.8924 (t80) cc_final: 0.8683 (t80)
REVERT: E   82 GLN cc_start: 0.7691 (tp40) cc_final: 0.7330 (tp40)
REVERT: E   83 MET cc_start: 0.7998 (ptp) cc_final: 0.7741 (ptp)
REVERT: D   47 GLU cc_start: 0.8065 (pm20) cc_final: 0.7704 (pm20)
  outliers start: 16
  outliers final: 9
  residues processed: 211
  average time/residue: 0.2215
  time to fit residues: 63.7352
Evaluate side-chains
  180 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 2.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  211 ILE
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  290 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 85 optimal weight:   20.0000
   chunk 77 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    2.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 266 HIS
** E  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.161890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112310 restraints weight = 37449.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.118446 restraints weight = 12680.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.121806 restraints weight = 6845.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3548
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8388  Z= 0.183
  Angle     :  0.640  11.175  11377  Z= 0.333
  Chirality :  0.045   0.189   1278
  Planarity :  0.004   0.039   1444
  Dihedral  :  9.509 179.796   1155
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.23 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.26), residues: 1025
  helix:  1.03 (0.25), residues: 424
  sheet: -0.50 (0.33), residues: 215
  loop : -0.60 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.009   0.001   HIS F  53 
 PHE   0.021   0.002   PHE B 235 
 TYR   0.014   0.001   TYR F 194 
 ARG   0.006   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  435)
  hydrogen bonds       : angle       4.83580 ( 1251)
  SS BOND              : bond        0.00614 (    3)
  SS BOND              : angle       4.39987 (    6)
  covalent geometry    : bond        0.00410 ( 8385)
  covalent geometry    : angle       0.63245 (11371)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 170
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  271 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8816 (mm)
REVERT: F  333 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7890 (m-10)
REVERT: A   33 ASP cc_start: 0.8363 (t0) cc_final: 0.7950 (t0)
REVERT: A  249 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7593 (p0)
REVERT: A  253 TYR cc_start: 0.7412 (m-80) cc_final: 0.6717 (m-80)
REVERT: A  356 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8212 (mtm180)
REVERT: B   45 MET cc_start: 0.8684 (mtm) cc_final: 0.8417 (mtm)
REVERT: B  214 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6951 (ptp-170)
REVERT: B  228 ASP cc_start: 0.7721 (m-30) cc_final: 0.7429 (m-30)
REVERT: B  234 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8214 (t80)
REVERT: E    4 LEU cc_start: 0.8119 (mt) cc_final: 0.7819 (mt)
REVERT: E   29 PHE cc_start: 0.9134 (t80) cc_final: 0.8779 (t80)
REVERT: E   82 GLN cc_start: 0.7630 (tp40) cc_final: 0.7272 (tp40)
REVERT: E   83 MET cc_start: 0.7987 (ptp) cc_final: 0.7559 (ptp)
REVERT: E   98 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7906 (tmm-80)
REVERT: D   47 GLU cc_start: 0.8111 (pm20) cc_final: 0.7670 (pm20)
  outliers start: 35
  outliers final: 18
  residues processed: 193
  average time/residue: 0.3186
  time to fit residues: 83.8042
Evaluate side-chains
  185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   50 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
E  35 ASN
E  77 ASN
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.158972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109019 restraints weight = 40999.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115530 restraints weight = 13236.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.118123 restraints weight = 7103.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   8388  Z= 0.245
  Angle     :  0.677  11.485  11377  Z= 0.354
  Chirality :  0.046   0.202   1278
  Planarity :  0.004   0.043   1444
  Dihedral  :  9.539 177.261   1155
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 19.71 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.27), residues: 1025
  helix:  1.10 (0.25), residues: 423
  sheet: -0.49 (0.33), residues: 228
  loop : -0.53 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.012   0.002   HIS A 357 
 PHE   0.021   0.002   PHE E 108 
 TYR   0.022   0.002   TYR F 194 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04982 (  435)
  hydrogen bonds       : angle       4.89877 ( 1251)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       4.52245 (    6)
  covalent geometry    : bond        0.00555 ( 8385)
  covalent geometry    : angle       0.66927 (11371)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   76 LEU cc_start: 0.8461 (mt) cc_final: 0.8217 (mp)
REVERT: F  160 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7880 (tm-30)
REVERT: F  214 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7124 (m-80)
REVERT: F  271 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8807 (mm)
REVERT: F  333 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7917 (m-10)
REVERT: A   33 ASP cc_start: 0.8438 (t0) cc_final: 0.8032 (t0)
REVERT: A  249 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7483 (p0)
REVERT: B  211 TRP cc_start: 0.7762 (m100) cc_final: 0.7560 (m100)
REVERT: B  214 ARG cc_start: 0.7237 (mtm180) cc_final: 0.7010 (ptp-170)
REVERT: B  234 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8164 (t80)
REVERT: B  264 TYR cc_start: 0.8669 (m-10) cc_final: 0.8274 (m-10)
REVERT: E   43 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7539 (ptpt)
REVERT: E   83 MET cc_start: 0.7876 (ptp) cc_final: 0.7512 (ptp)
REVERT: E   98 ARG cc_start: 0.8518 (ttp80) cc_final: 0.7953 (tmm-80)
REVERT: E  106 ASP cc_start: 0.8390 (p0) cc_final: 0.8073 (p0)
REVERT: D   47 GLU cc_start: 0.8183 (pm20) cc_final: 0.7680 (pm20)
  outliers start: 42
  outliers final: 34
  residues processed: 191
  average time/residue: 0.2842
  time to fit residues: 73.4113
Evaluate side-chains
  196 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  132 GLU
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   50 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 76 optimal weight:    9.9990
   chunk 67 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 60 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 90 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN    B
B 266 HIS
E  35 ASN
E  74 ASN
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.161459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112109 restraints weight = 34799.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.118144 restraints weight = 12738.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.121503 restraints weight = 6895.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8388  Z= 0.155
  Angle     :  0.612  11.544  11377  Z= 0.316
  Chirality :  0.044   0.219   1278
  Planarity :  0.004   0.044   1444
  Dihedral  :  9.448 178.591   1155
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.08 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.27), residues: 1025
  helix:  1.33 (0.26), residues: 418
  sheet: -0.24 (0.35), residues: 213
  loop : -0.61 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 281 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.032   0.002   PHE E  29 
 TYR   0.022   0.001   TYR F 194 
 ARG   0.004   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  435)
  hydrogen bonds       : angle       4.65397 ( 1251)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       3.84275 (    6)
  covalent geometry    : bond        0.00343 ( 8385)
  covalent geometry    : angle       0.60607 (11371)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   76 LEU cc_start: 0.8502 (mt) cc_final: 0.8273 (mp)
REVERT: F  160 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: F  210 MET cc_start: 0.6529 (mtp) cc_final: 0.6226 (ttm)
REVERT: F  214 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7055 (m-80)
REVERT: F  271 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8818 (mm)
REVERT: F  333 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7702 (m-10)
REVERT: A  249 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7361 (p0)
REVERT: B   37 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8058 (mp)
REVERT: B  188 MET cc_start: 0.8324 (mmm) cc_final: 0.8060 (mmt)
REVERT: B  211 TRP cc_start: 0.7711 (m100) cc_final: 0.7396 (m100)
REVERT: B  214 ARG cc_start: 0.7239 (mtm180) cc_final: 0.6957 (ttp-170)
REVERT: B  235 PHE cc_start: 0.8902 (t80) cc_final: 0.8490 (t80)
REVERT: B  262 MET cc_start: 0.6820 (ttm) cc_final: 0.6447 (ttm)
REVERT: E   33 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7744 (ptpt)
REVERT: E   43 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7550 (ptpt)
REVERT: E   77 ASN cc_start: 0.7413 (t0) cc_final: 0.7136 (t0)
REVERT: E   83 MET cc_start: 0.7811 (ptp) cc_final: 0.7418 (ptp)
REVERT: E   98 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7828 (tmm-80)
REVERT: E  106 ASP cc_start: 0.8326 (p0) cc_final: 0.8066 (p0)
REVERT: D   47 GLU cc_start: 0.8103 (pm20) cc_final: 0.7545 (pm20)
  outliers start: 33
  outliers final: 22
  residues processed: 197
  average time/residue: 0.2214
  time to fit residues: 58.9770
Evaluate side-chains
  191 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   50 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    0.1980
   chunk 94 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 90 optimal weight:    1.9990
   overall best weight:    2.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.159667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.112941 restraints weight = 46739.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.117271 restraints weight = 13656.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.120997 restraints weight = 8031.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8388  Z= 0.198
  Angle     :  0.653  11.212  11377  Z= 0.336
  Chirality :  0.046   0.234   1278
  Planarity :  0.004   0.046   1444
  Dihedral  :  9.474 178.343   1155
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 21.97 %
    Favored  : 72.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.27), residues: 1025
  helix:  1.28 (0.26), residues: 419
  sheet: -0.30 (0.35), residues: 216
  loop : -0.61 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 281 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.027   0.002   PHE E  29 
 TYR   0.024   0.002   TYR F 194 
 ARG   0.005   0.000   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04624 (  435)
  hydrogen bonds       : angle       4.68402 ( 1251)
  SS BOND              : bond        0.00581 (    3)
  SS BOND              : angle       3.82291 (    6)
  covalent geometry    : bond        0.00447 ( 8385)
  covalent geometry    : angle       0.64706 (11371)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 172
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   76 LEU cc_start: 0.8515 (mt) cc_final: 0.8269 (mp)
REVERT: F  160 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7983 (tm-30)
REVERT: F  210 MET cc_start: 0.6724 (mtp) cc_final: 0.6490 (ttm)
REVERT: F  214 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7159 (m-80)
REVERT: F  271 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8815 (mm)
REVERT: F  333 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7834 (m-10)
REVERT: A   60 MET cc_start: 0.8412 (mmm) cc_final: 0.8107 (mmm)
REVERT: A  249 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7516 (p0)
REVERT: B   37 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8104 (mp)
REVERT: B  211 TRP cc_start: 0.7764 (m100) cc_final: 0.7513 (m100)
REVERT: B  214 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6910 (ttp-170)
REVERT: B  235 PHE cc_start: 0.8973 (t80) cc_final: 0.8649 (t80)
REVERT: B  254 ASP cc_start: 0.8376 (t70) cc_final: 0.8056 (t0)
REVERT: B  264 TYR cc_start: 0.8460 (m-80) cc_final: 0.8098 (m-80)
REVERT: E   43 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7542 (ptpt)
REVERT: E   77 ASN cc_start: 0.7578 (t0) cc_final: 0.7288 (t0)
REVERT: E   82 GLN cc_start: 0.7643 (tp40) cc_final: 0.7400 (tp40)
REVERT: E   83 MET cc_start: 0.7768 (ptp) cc_final: 0.7422 (ptp)
REVERT: E   98 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8050 (tmm-80)
REVERT: E  106 ASP cc_start: 0.8325 (p0) cc_final: 0.8020 (p0)
REVERT: D   47 GLU cc_start: 0.7995 (pm20) cc_final: 0.7544 (pm20)
  outliers start: 44
  outliers final: 32
  residues processed: 200
  average time/residue: 0.2115
  time to fit residues: 57.9742
Evaluate side-chains
  199 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 162
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  116 VAL
Chi-restraints excluded: chain F residue  132 GLU
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   50 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN    B
B 266 HIS
E  35 ASN
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.159834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.111174 restraints weight = 35957.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.117342 restraints weight = 12683.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.120163 restraints weight = 6696.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3521
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3521 r_free = 0.3521    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3521 r_free = 0.3521    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3521
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8388  Z= 0.139
  Angle     :  0.612  11.189  11377  Z= 0.313
  Chirality :  0.044   0.253   1278
  Planarity :  0.004   0.048   1444
  Dihedral  :  9.405 179.952   1155
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 24.01 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 1025
  helix:  1.49 (0.26), residues: 419
  sheet: -0.01 (0.36), residues: 203
  loop : -0.65 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E  47 
 HIS   0.007   0.001   HIS F  53 
 PHE   0.025   0.001   PHE E  29 
 TYR   0.025   0.001   TYR F 194 
 ARG   0.007   0.000   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04230 (  435)
  hydrogen bonds       : angle       4.52390 ( 1251)
  SS BOND              : bond        0.00433 (    3)
  SS BOND              : angle       3.51304 (    6)
  covalent geometry    : bond        0.00305 ( 8385)
  covalent geometry    : angle       0.60685 (11371)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 173
  time to evaluate  : 1.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   76 LEU cc_start: 0.8603 (mt) cc_final: 0.8382 (mp)
REVERT: F  160 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: F  214 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.6866 (m-10)
REVERT: F  271 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8821 (mm)
REVERT: F  333 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7908 (m-10)
REVERT: A  249 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7403 (p0)
REVERT: B  124 TYR cc_start: 0.8789 (m-80) cc_final: 0.8462 (m-80)
REVERT: B  211 TRP cc_start: 0.7664 (m100) cc_final: 0.7273 (m100)
REVERT: B  234 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7691 (t80)
REVERT: B  235 PHE cc_start: 0.8933 (t80) cc_final: 0.8623 (t80)
REVERT: B  254 ASP cc_start: 0.8499 (t70) cc_final: 0.8142 (t0)
REVERT: B  264 TYR cc_start: 0.8347 (m-80) cc_final: 0.8023 (m-80)
REVERT: E   33 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7595 (ptpt)
REVERT: E   77 ASN cc_start: 0.7632 (t0) cc_final: 0.7326 (t0)
REVERT: E   83 MET cc_start: 0.7781 (ptp) cc_final: 0.7374 (ptp)
REVERT: E   98 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7864 (tmm-80)
REVERT: E  106 ASP cc_start: 0.8332 (p0) cc_final: 0.7926 (p0)
REVERT: D   47 GLU cc_start: 0.8054 (pm20) cc_final: 0.7744 (pm20)
  outliers start: 37
  outliers final: 25
  residues processed: 194
  average time/residue: 0.2949
  time to fit residues: 79.6913
Evaluate side-chains
  196 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 165
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  132 GLU
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  325 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0020
   chunk 44 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0670
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0370
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.3404

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.165227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.119282 restraints weight = 36582.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.124398 restraints weight = 11907.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129194 restraints weight = 6693.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8388  Z= 0.118
  Angle     :  0.626  10.447  11377  Z= 0.313
  Chirality :  0.044   0.258   1278
  Planarity :  0.004   0.070   1444
  Dihedral  :  9.235 177.546   1155
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 27.07 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 1025
  helix:  1.73 (0.26), residues: 412
  sheet:  0.08 (0.36), residues: 204
  loop : -0.64 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  47 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.025   0.001   PHE E  29 
 TYR   0.023   0.001   TYR F 194 
 ARG   0.006   0.000   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  435)
  hydrogen bonds       : angle       4.40777 ( 1251)
  SS BOND              : bond        0.00362 (    3)
  SS BOND              : angle       2.91309 (    6)
  covalent geometry    : bond        0.00246 ( 8385)
  covalent geometry    : angle       0.62229 (11371)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 183
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   76 LEU cc_start: 0.8472 (mt) cc_final: 0.8254 (mt)
REVERT: A  249 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7666 (p0)
REVERT: B  124 TYR cc_start: 0.8662 (m-80) cc_final: 0.8395 (m-80)
REVERT: B  211 TRP cc_start: 0.7594 (m100) cc_final: 0.7220 (m100)
REVERT: B  234 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7490 (t80)
REVERT: B  235 PHE cc_start: 0.8870 (t80) cc_final: 0.8468 (t80)
REVERT: B  254 ASP cc_start: 0.8406 (t70) cc_final: 0.8114 (t0)
REVERT: B  289 TYR cc_start: 0.8803 (m-80) cc_final: 0.8339 (m-80)
REVERT: E   33 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7820 (ptpt)
REVERT: E   77 ASN cc_start: 0.7572 (t0) cc_final: 0.7300 (t0)
REVERT: E   83 MET cc_start: 0.7758 (ptp) cc_final: 0.7311 (ptp)
REVERT: E   98 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7414 (tmm-80)
REVERT: E  106 ASP cc_start: 0.7953 (p0) cc_final: 0.7579 (p0)
  outliers start: 22
  outliers final: 13
  residues processed: 194
  average time/residue: 0.1971
  time to fit residues: 53.0370
Evaluate side-chains
  183 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 266 HIS
E  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.160070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.112708 restraints weight = 39330.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.118164 restraints weight = 13102.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.122611 restraints weight = 7472.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8388  Z= 0.167
  Angle     :  0.679  12.231  11377  Z= 0.340
  Chirality :  0.046   0.285   1278
  Planarity :  0.004   0.063   1444
  Dihedral  :  9.291 177.450   1155
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 28.20 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 1025
  helix:  1.59 (0.26), residues: 419
  sheet:  0.05 (0.37), residues: 187
  loop : -0.56 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 281 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.022   0.002   PHE E  29 
 TYR   0.020   0.001   TYR D  40 
 ARG   0.007   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04252 (  435)
  hydrogen bonds       : angle       4.48160 ( 1251)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       3.20707 (    6)
  covalent geometry    : bond        0.00380 ( 8385)
  covalent geometry    : angle       0.67567 (11371)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.8336 (mmm) cc_final: 0.7968 (mmm)
REVERT: A  249 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7745 (p0)
REVERT: B  211 TRP cc_start: 0.7682 (m100) cc_final: 0.7313 (m100)
REVERT: B  234 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7640 (t80)
REVERT: B  235 PHE cc_start: 0.8981 (t80) cc_final: 0.8541 (t80)
REVERT: B  254 ASP cc_start: 0.8441 (t70) cc_final: 0.8129 (t0)
REVERT: B  264 TYR cc_start: 0.8129 (m-80) cc_final: 0.7660 (m-80)
REVERT: B  289 TYR cc_start: 0.8955 (m-80) cc_final: 0.8408 (m-80)
REVERT: E   33 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7654 (ptpt)
REVERT: E   77 ASN cc_start: 0.7584 (t0) cc_final: 0.7263 (t0)
REVERT: E   83 MET cc_start: 0.7553 (ptp) cc_final: 0.7232 (ptp)
REVERT: E  106 ASP cc_start: 0.8174 (p0) cc_final: 0.7795 (p0)
  outliers start: 23
  outliers final: 20
  residues processed: 177
  average time/residue: 0.1904
  time to fit residues: 48.5445
Evaluate side-chains
  182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 159
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  297 TRP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 59 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 86 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 ASN
B 266 HIS
E  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.163030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.121064 restraints weight = 32760.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.123236 restraints weight = 12896.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124887 restraints weight = 9071.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3590
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3590 r_free = 0.3590    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3590 r_free = 0.3590    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3590
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8388  Z= 0.129
  Angle     :  0.672  10.954  11377  Z= 0.337
  Chirality :  0.045   0.296   1278
  Planarity :  0.004   0.067   1444
  Dihedral  :  9.240 176.013   1155
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 27.97 %
    Favored  : 69.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.27), residues: 1025
  helix:  1.74 (0.26), residues: 411
  sheet:  0.03 (0.37), residues: 181
  loop : -0.52 (0.32), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 281 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.023   0.001   PHE E  29 
 TYR   0.013   0.001   TYR F 194 
 ARG   0.007   0.000   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  435)
  hydrogen bonds       : angle       4.47868 ( 1251)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       2.94071 (    6)
  covalent geometry    : bond        0.00284 ( 8385)
  covalent geometry    : angle       0.66840 (11371)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  269 LYS cc_start: 0.8245 (tptt) cc_final: 0.7802 (ttpt)
REVERT: F  271 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8892 (mt)
REVERT: A   20 ARG cc_start: 0.8916 (mtm110) cc_final: 0.8679 (mtm110)
REVERT: A  249 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7652 (p0)
REVERT: B  124 TYR cc_start: 0.8739 (m-80) cc_final: 0.8433 (m-80)
REVERT: B  211 TRP cc_start: 0.7621 (m100) cc_final: 0.7284 (m100)
REVERT: B  235 PHE cc_start: 0.8929 (t80) cc_final: 0.8638 (t80)
REVERT: B  254 ASP cc_start: 0.8491 (t70) cc_final: 0.8174 (t0)
REVERT: B  289 TYR cc_start: 0.8816 (m-80) cc_final: 0.8241 (m-80)
REVERT: E   33 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7663 (ptpt)
REVERT: E   77 ASN cc_start: 0.7525 (t0) cc_final: 0.7198 (t0)
REVERT: E  106 ASP cc_start: 0.8229 (p0) cc_final: 0.7983 (p0)
  outliers start: 19
  outliers final: 16
  residues processed: 179
  average time/residue: 0.1956
  time to fit residues: 48.6466
Evaluate side-chains
  184 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  325 SER
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  297 TRP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 52 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.160156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.113329 restraints weight = 44535.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.118979 restraints weight = 13135.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.122259 restraints weight = 7502.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8388  Z= 0.168
  Angle     :  0.675  11.089  11377  Z= 0.343
  Chirality :  0.045   0.286   1278
  Planarity :  0.004   0.071   1444
  Dihedral  :  9.273 175.661   1155
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 28.09 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.27), residues: 1025
  helix:  1.61 (0.26), residues: 417
  sheet: -0.08 (0.37), residues: 186
  loop : -0.54 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 281 
 HIS   0.008   0.001   HIS B 225 
 PHE   0.020   0.002   PHE E  29 
 TYR   0.015   0.001   TYR D  40 
 ARG   0.007   0.000   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04296 (  435)
  hydrogen bonds       : angle       4.50859 ( 1251)
  SS BOND              : bond        0.00360 (    3)
  SS BOND              : angle       3.24716 (    6)
  covalent geometry    : bond        0.00383 ( 8385)
  covalent geometry    : angle       0.67140 (11371)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3881.52 seconds
wall clock time: 72 minutes 49.31 seconds (4369.31 seconds total)